Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis

In the Morhardt Lab, we use zebrafish as an animal model to study bladder development and function. We've identified a functional urinary bladder that fills and empties in zebrafish. While zebrafish are small, we sought to take advantage of its size to economically utilize spatial transcriptomic techniques and our understanding of the vertebrate bladder.

Spatial transcriptomic techniques can quickly become expensive if reagents and equipment are not optimized. This protocol provides a proven technique to achieve this using zebrafish and provides the insights into the expected results and mitigation of problems that may arise as a result of the technology. Besides the economic utilization of expensive spatial transcriptomic technologies, this work has allowed us to perform large scale spatial transcriptomic analyses of essentially whole organs across several ages while minimizing batch effects.